Processes of membrane systems with promoters and inhibitors

Kleijn, Jetty; Koutny, Maciej

doi:10.1016/j.tcs.2008.04.006

Cited by 9 publications

(5 citation statements)

References 15 publications

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“…In this section we recall how to associate a membrane system to a zero safe Petri net and then how evolutions in membrane systems and those in a zero safe nets are related. We follow closely what has been developed by [7], adapting it to our setting. To each rule we associate a transition (which are indexed by the name of the rule and by the compartment), whereas places are associated to objects.…”

Section: From Membrane Systems To Petri Netsmentioning

confidence: 99%

“…Each locality identifies a distinct set of transitions which may only be executed synchronously, i.e., in a locally maximal concurrent manner; and a notion of process for these nets is developed, with the associated notion of dependency. This is further studied and cast in a more general framework in [7]. We develop a Petri net view of membrane systems which is, differently from other approaches, based on zero safe nets [2].…”

Section: Introductionmentioning

confidence: 99%

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Dependencies and Simultaneity in Membrane Systems

Pinna¹,

Saba²

2009

Electron. Proc. Theor. Comput. Sci.

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Membrane system computations proceed in a synchronous fashion: at each step all the applicable rules are actually applied. Hence each step depends on the previous one. This coarse view can be refined by looking at the dependencies among rule occurrences, by recording, for an object, which was the a rule that produced it and subsequently (in a later step), which was the a rule that consumed it. In this paper we propose a way to look also at the other main ingredient in membrane system computations, namely the simultaneity in the rule applications. This is achieved using zero-safe nets that allows to synchronize transitions, i.e., rule occurrences. Zero-safe nets can be unfolded into occurrence nets in a classical way, and to this unfolding an event structure can be associated. The capability of capturing simultaneity of zero-safe nets is transferred on the level of event structure by adding a way to express which events occur simultaneously.

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Section: From Membrane Systems To Petri Netsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dependencies and Simultaneity in Membrane Systems

Pinna¹,

Saba²

2009

Electron. Proc. Theor. Comput. Sci.

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“…In order to capture the compartmental structure and the locally maximal parallel behavior of membrane systems, localities and a locally maximal concurrent semantics were introduced and investigated for Petri nets in [9]. Furthermore, Petri nets with localities were also used to describe membrane creation and membrane dissolution in [8] and extended in [7] to model the use of promoters and inhibitors. For more details on the specific membrane system models and their computational power, see the handbook [14,20,21] for more recent developments.…”

Section: Introductionmentioning

confidence: 99%

Description of membrane systems with time Petri nets: promoters/inhibitors, membrane dissolution, and priorities

Battyányi

Vaszil

2020

J Membr Comput

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We continue the investigations of the connection between membrane systems and time Petri nets by extending the examined class of systems from simple symbol-object membrane systems to more complex cases: rules with promoters/inhibitors, membrane dissolution, and priority relation on the rules. By constructing the simulating time Petri net, we retain one of the main characteristics of the Petri net model; namely, the firings of the transitions can take place in any order, and there is no need to introduce maximal parallelism in the Petri net semantics. Instead, we substantially exploit the gain in computational strength obtained by the introduction of the timing feature for Petri nets.

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“…The modelling power of PTL-nets (even after enhancing them with inhibitor and activator arcs in [7]) was constrained by the fact that each transition belonged to a unique locality, and therefore localities were all non-overlapping. In this paper, we drop this restriction aiming at a net model which we feel could provide a greater scope for faithful (or direct) modelling features implied by the complex nature of, for example, modern VLSI systems or biological systems.…”

Section: Introductionmentioning

confidence: 99%

Synthesis Problem for Petri Nets with Localities

Koutny

Pietkiewicz-Koutny

2012

Lecture Notes in Computer Science

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There is a growing need to introduce and develop computational models capable of faithfully modelling systems whose behaviour combines synchrony with asynchrony in a variety of complicated ways. Examples of such real-life systems can be found from VLSI hardware to systems of cells within which biochemical reactions happen in synchronised pulses. One way of capturing the resulting intricate behaviours is to use Petri nets with localities partitioning transitions into disjoint groups within which execution is synchronous and maximally concurrent. In this paper, we generalise this type of nets by allowing each transition to belong to several localities. Moreover, we define this extension in a generic way for all classes of nets defined by net-types. The semantics of nets with overlapping localities can be defined in different ways, and we here discuss four fundamental interpretations, each of which turns out to be an instance of the general model of nets with policies. Thanks to this fact, it is possible to automatically synthesise nets with localities from behavioural specifications given in terms of finite transition systems. We end the paper outlining some initial ideas concerning net synthesis when the association of transitions to localities is not given and has to be determined by the synthesis algorithm.

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Processes of membrane systems with promoters and inhibitors

Cited by 9 publications

References 15 publications

Dependencies and Simultaneity in Membrane Systems

Dependencies and Simultaneity in Membrane Systems

Description of membrane systems with time Petri nets: promoters/inhibitors, membrane dissolution, and priorities

Synthesis Problem for Petri Nets with Localities

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